The way police record "non-crime hate incidents" against transgender people has "a chilling effect" on freedom of expression, the High Court has heard.
Former police officer Harry Miller was contacted by Humberside Police in January following a complaint over alleged transphobic tweets.
The court heard he was told he had not committed a crime, but his post was being recorded as a "hate incident".
He is taking action against the College of Policing and Humberside Police.
Mr Miller, from Lincolnshire, claims the guidelines breached his human rights to freedom of expression.
In response, officials said the guidance was lawful and caused no interference with his rights.
'Legitimate public debate'
He previously described police as using George Orwell's novel 1984 as an "operating manual".
His barrister, Ian Wise QC, told the court his client was "deeply concerned" about proposed reforms to the law on gender recognition and had used Twitter to "engage in debate about transgender issues".
Mr Wise said Humberside Police had also sought to "dissuade him from expressing himself on such issues in the future".
This, he said, was "contrary to his fundamental right to freedom of expression".
Mr Miller has "never expressed hatred towards the transgender community", he said.
"He has simply questioned the belief that trans women are women and should be treated as such for all purposes."
His views, he added, "form part of a legitimate public debate and cannot sensibly be regarded as 'hate speech'".
In response, Jonathan Auburn, for the College of Policing, said: "While the claimant now expressly disavows having any personal hostility or prejudice towards transgender people, his social media messages speak for themselves."
In one tweet, he said Mr Miller posted: "I was assigned mammal at birth, but my orientation is fish. Don't mis-species me."
The hearing is expected to last for two days.